Changes in the Wind: Indigo Leaves
by Teddi 8347
Summary: An organization took over the Pokémon World. People are resisting them. However, it seems to be a losing battle. After discovering their plans to time travel and take over the world sooner, a man name Phoenix decides to go back in time to stop them. Unfortunately, they caught him. Who would save the world now? Rated for saftey.
1. Prologue One: The End of Time

I wrote this about a year ago. I'm not proud of it. I might redo it someday, if I have the insperation for it. I DO NOT OWN POKEMON!

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Data File ASKPD1846382: The Pokémon World has been taken over by a team called Team Cryptic and they now own everyone in the sense of power and money. No one has been able to take them down and those who tried had either disappeared mysteriously or are too traumatize to communicate. There are reports of a group of resistance fighting to free the Pokémon World. However there is no current evidence that proves that their cause is not in vain.

Many people have tried to stop them: law enforcement, the Elites and Champions, the Frontiers, Gym Leaders, Team Rocket, Team Aqua, Team Magma, Team Galactic and Team Plasma. As well as high level Pokémon Trainers but none of them has been able to put a dent into them. Most have their families take from them and are never seen again.

A mysterious thing happened one day. People who were missing suddenly appear. They claim they were rescued by a phantom. No one knows who or what this phantom is or what their goals are. For the most part, it seems to be against Team Cryptic but the information is very limited. I, however, found a way to contact this phantom but I had never used it before, nor do I hope to ever use it.

There is someone who seems to always come back and fight no matter the lost. The name: Sunlight Phoenix, the last hope for all but he is better known as the Shadow of the Phoenix. His mission: To stop these criminals and to bring peace to the world once more. No one knows how he does what he does but he is the reason the people still fight.

I know him better than anyone for I am his partner in crime. I can hack into computers and copy high secured files without fail. I hold the information that could bring these criminals down. I can also manipulate electronics for short seconds. Very useful if you're a thief, this is what Phoenix is… kind of. All the known information about this team is with us. Speaking of which, time to work my magic.

**Hacking Team Cryptic Computer Data Base... Copying Files To Hard drive… Copying The Cryptic Files… Saving… Encrypting Data Files… Activating Fire Walls… Activating Emergency Firewalls… Saving Backup…Done. Now Get Out Of Here Before The Alarm Goes Off. 30 Seconds.**

Phoenix didn't need to be told twice and was out of the room to make his escape. Using the Ninja abilities he learned some time ago, he fades into the shadows. **20 Seconds.** He moved swiftly, and quietly, down the halls and past the guards. It's unfortunate that the central computer, where the data was stored, is so deep in the base, and the security was so high he needed contact to get the information out. Phoenix actually has doubts that he would make it out of here in time.

**15 Seconds.** As he comes to the main hallway, Phoenix changed into a disguise and mimics the people there while still moving quickly to the exit but not enough to draw attention to himself. Once he was out of sight he uses his aura and ninja skills to move faster and to not be seen. He climbs in the air vent that had brought him this far in and started to use his aura to silent his movements.

**5 Seconds.** Phoenix moves faster though the vents. He moves to a blind spot and waited for the signal his friend would give him when it is safe to move again. He hopes his friend could keep the lasers offline and not draw suspicion to the vents. Then he braced himself for the alarms.

As expected the Alarms blared loudly and the people who work there got into action. And, as expected, the air vents became the worst escape route. And he wasn't expecting the workers to move so fast. Fortunately for Phoenix, his friend hacked into the security systems and brought the lasers offline and he waited for the coast to clear. Once he was out of the vent's he work his way to the door that would lead him outside, though he knew he wouldn't be out of the woods until he is out of the woods, or forest to be exact.

Phoenix moves quickly and silently through the halls towards the door. His senses told him to stop and, when he did, a guard doing his rounds, walks right past him. Phoenix thought for a moment to whether let the guard be or knock him out. Knocking the guard out would signal the others that he is there but leaving him alone would mean less time to escape. Either way is risky, too risky.

He finally knocks the guy out and hides him in a closet. Why they have a closet in the hall, Phoenix doesn't know. It would have made more sense if there was something in there. Then he moves to the door and have his friend disable the door alarm. Once outside, Phoenix ran full force into the dense forest to lose them. He was lucky that it is raining hard so tracking him is going to be even harder. He ran for a minute before stopping to sit down and rest.

**"You Really Shouldn't Rest Here,"** a male electronic voice said to Phoenix. The man pulls out a small handheld computer and looks at it.

"I know, friend, but I used too much energy in there. Besides we are miles away from the base and the forest is so thick it would take them a while to get here." Phoenix closes his eyes for his Aura Sight to work. While he could see life, none of it was Pokémon. Since Team Cryptic took over Pokémon had become scarce. Phoenix worries about this. It is one of the many reasons why he fights.

**"Would You Like To See The Data I've Collected,"**the small computer asks though he knew the answer. Phoenix takes a look at the computer and presses some buttons. The computer thoughts went back to when this man became Phoenix. All of his friends had either died, suffered a loss or had been tortured beyond saving, usually mentally. Phoenix appearance also had changed for his hair is now ash white and his eyes are void of emotion. They have been this way since the death of his most trusted partner and brother. It has gotten worst with every fight he had been in, seen or heard and death of those he once knew.

"This can't be right," the man mutters as he looks at the information. This brought the computer back from its thoughts. One would not think a computer has thoughts but it is no longer just a computer. It, or more he, didn't ask what the problem is because he knew having to read everything he downloaded. Trust me; there are things on that file that is better left untouched.

**"Pretty Unbelievable, Right?"**the small computer commented. The man just looks though the list, trying to understand what it is he saw. Of course his computer friend would only let him see the most important stuff, not that Phoenix knew.

"I don't believe it. They plan to travel through time? Why and how would they do that?" the man asks disbelief and worry evident in his voice. The computer shows him the plans and documents they have. Once again, Phoenix went into reading.

**"We Should Get Going Phoenix,"**the computer spoke while using his tracking sensors to track Team Cryptic. As well as a blocking signal so the enemy couldn't trace them. The one thing that's worries the computer are their heat signals. No doubt Team Cryptic would use heat sensors to find them. Phoenix nods as he stood up. He puts the computer away and covers himself in mud since the rain has died down enough. The mud should mask his heat long enough for him to get away.

"Then let's get going." Once again, Phoenix uses his aura and ninja skills to pick up speed and not leave tracks. He went one step farther and created copies of himself and let them run in different directions to try to confuse the enemy. His senses told him they were still in the clear.

"I can't believe they have the technology and the Pokémon to do this. If they succeed then they would win. I won't allow that. If I can't stop them before they put their plan into motion than I will follow them and stop them before they become a threat." Phoenix blood boils at the thought. His friend knew he wouldn't stand for this but he also knew Phoenix can't do this alone.

**"Would You Like Me To Find A Way To Contact The Phantom?"**the computer asks. It's a simple question, really but there is a problem; no one knows who the Phantom is. Phoenix is also having a hard time deciding. On the one hand it would be nice to have help but on the other hand is they could be working for the enemy and he would be walking into a trap. As much as he wants, or needs, help he doesn't want to take a risk.

"Only contact this Phantom if anything were to happen to me that I can't handle. I don't want to take the risk beforehand." If it could the computer would nod in understanding. Phoenix use a signal to tell his friend it was time to be quiet. Good thing too since a Team Cryptic member walked right by. Since the member couldn't see anything they walked right past and went away.

It took hours for Phoenix to walk to the edge of the forest. His computer friend told him to be careful since they don't have an escape vehicle and the enemy has deployed helicopters to search for him. The worst part about this is Phoenix doesn't have any Pokémon to help him escape while Team Cryptic has Pokémon to track down trespassers. Since they took over the world, only Team Cryptic members can have Pokémon, not that many resistance members listen. Still, he has no Pokémon to defend himself with. To make matters worse, a thunderstorm started brewing and it looks like it's going to be a bad one.

"PHOENIX! WE HAVE YOU SURROUNDED! SURENDER NOW OR WE WILL SHOW NO MERCY!" a voice for one of the helicopters boomed overhead with their spotlight on him. Thunder crackled through the air as Phoenix mutters to himself about his luck. How they were able to locate him was unknown to Phoenix and his computer friend but they did and now it is a race against time to escape.

The storm also seem to be getting stronger for the winds have pick up, the rain turned into a down pour again and the lightning is right above them. The helicopter seems to be struggling in the high winds but somehow manage to keep the spotlight on him. More men in vehicles appear and surround him. As Phoenix prepares an Aura Sphere, lightning strikes the helicopter, making it crash.

It was a crazy battle; lightning kept on striking everything but the rain is falling so hard that none of the vegetation caught on fire. Phoenix did his best to get out but in the end they caught him. However in a last ditch effort he threw his computer as hard and as far as he could. Then they dragged him back to their base. One inside, a commander walks up to the group and looks straight at Phoenix.

"Well done, everyone, in capturing our most feared foe," The commander spoke with such a heavenly voice it's scary. Phoenix did his best to not look up. This made the commander chuckle.

"Not talking I see. What's the matter Phoenix? Upset you lost?" A taunt, trying to make him break; what are they thinking. After everything he's been through it would take a lot more than just a taunt. The commander isn't dumb and saw this.

"Well, no matter. I suppose you know of our plans to time travel. Even if you don't, let me enlighten you, it's not like you are leaving anytime soon." Even though his eyes never left the floor, he was listening. It's not every day an enemy would tell you their plans and it's not like he has anything better to do anyway.

"You see, Time travel has always been in our plans. To take over the world sooner and sooner until we have control over time itself. As you are pretty much aware, if you change one thing in the past then everything for the future would unravel. And Team Cryptic has the power the knit the future into what we see fit! Unfortunately, this time proved to be a little bit difficult. So much of our resources have been drained trying to fight the resistance and you weren't of any help." Phoenix couldn't help but smile at this. It was great to hear he made things difficult for them.

The commander continues. "However we can still go back in time, just not as far as we would have liked but far enough. Now, imagine if we were to take a very powerful trainer before they even knew what a Pokémon is and raise them." The commander smiled when Phoenix's body stiffened.

"I see you are beginning to understand, Phoenix. You see, the trainer who I think would be the best choice is none other than Ash Ketchum." Phoenix's head shot up and his eyes locked with the commander. This made the commander smile now that Phoenix has given his full attention.

"I'm glad to have your full attention. I suppose I don't have to tell you the rest, unless you really want me to." Phoenix gritted his teeth, trying to hold back his anger. It wasn't working very well.

"And what makes you think it would work?" he asks. The commander just chuckled before walking right to his face. This was to close for Phoenix's comfort but he held on, not wanting them to know. The commander stops right at his ear.

"Because we have done this before," was the whispered answer that Phoenix never wanted to hear. The commander just smiled before ordering the grunts to put Phoenix in a holding cell. Phoenix didn't want to give up. His mind was trying to find a solution to this problem.

"You'll never get away with this," he yells as they drag him away. The commander just smiled and let out a heavenly laugh.

"And who is going to stop us now that we have you; your little computer? It doesn't have the resources to operate on its own and the people here are too weak without your guidance." And with that, the commander left with Phoenix trying to think of a plan but he knew it was no use. He only wished that someone would stop them before it was too late.

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Unbeknownst to everyone there, a Ghost Pokémon heard everything and leaves the building. Outside the storm was still raging but not as bad as before. The Ghost Pokémon moves to a faraway clearing to where some Pokémon have gathered. Then he tells them what he heard.

All of the Pokémon where shock and scared. Many of them started panicking. Before things got out of hand, a Butterfree, that has jewels to indicate he is a Guardian Pokémon, came up and calms everyone down. Once everyone has settled down, another Pokémon came up and told them what they would do. None of them argues since this is the only plan they have. Then that Pokémon turns to face Team Cryptic's building.

**"Don't worry Dexter. The Phantoms never leave a member behind. Even if the member doesn't know,"** it said while gripping the computer it found. Thunder roared across the land as the Pokémon turns around and leaves to set the plan in motion.

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What do you think? Please leave a review.


	2. Prologue Two: The Change in Destiny

**A/N: I DON'T OWN POKEMON!**

**Okay, so this isn't the best chapter, I got bored writing it. It would help if you, the readers, could say what I need to improve on. I am still writing the first chapter so don't expect it to come soon. I might write it sooner if you'll review and give suggestions.**

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It's a quiet but stormy night in the town of Pallet. Okay, so the storm was anything but quiet but the town's activity was quiet. Alright, so the storm kept most everyone inside but that's not the point! The point is no one is outside and there is a storm, now let me continue the 'story'!

There is a house somewhere in Pallet Town where… WOULD YOU STOP INTERUPTING ME?! No, I don't know where the house is, exactly. But, I do know it's a two-story house with a magnificent garden all around it. A friend told me! Now, BE QUIET AND HELP ME LOOK!

Now… where was I? What? NO! I DON'T MEAN THE LAST PLACE I WAS! I'M TALKING ABOUT THE 'STORY'! Okay, you are no fun! I'm trying to lighten the mood by narrating what's happening at the moment; IDON'T NEED A REMINDER ON WHAT WE ARE DOING, WHY WE ARE HERE AND WHAT WOULD HAPPEN IF WE DON'T SUCCEED! I'm glad you understand; now let me narrate IN PEACE!

Thank you. Let me start over. It's a stormy night in the town of Pallet. Only those who brave the storm are out tonight. There is a house somewhere that has something we need, something special. And we need to get there before… You found it? GREAT! Is there anyone inside? The one we are looking for is in there, right? So he is all alone. Perfect, let's put this plan into motion.

You know the deal, I go in and you keep watch. When you see 'them,' call the police and tell them to come quietly. Then tell me so we can leave. 'They' must not succeed this time. I know you don't need a reminder: I'm just saying how important this is. Ok, you know what? Let's just forget this conversation and do our jobs. ALL RIGHT, I'M GOING!

As a friend said, the house has a magnificent garden only not how they describe it. The storm is still raging on but I don't care. Then again, it would be hard to see 'them' coming. I don't have time for this; I have to find the boy. Finding the room was easier than I thought. The boy is there and it looks like he is about to sleep. Things couldn't be better, now I just have to wait until he falls asleep. It won't be long, Ask Ketchum.

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4-year-old Ash Ketchum was home alone when the storm arrived. His mother was working late at the family own restaurant so Ash had the house all to himself and he would have loved it if Gary was over. But their moms didn't like the idea of the two boys being in a house alone all night. Pulling his thoughts away from the loneliness, Ash turns the TV on and sits down on his bed.

He watches a cartoon show about the First Pokémon Master, Red. It wasn't long until Ash was acting along. After an hour he got ready for bed but the thought about being alone in the house with a thunderstorm outside kept him up. So he put a movie in about Red and fell asleep watching it. He never knew eyes were watching him as he drifted into dreamland.

The dream Ash was having is him being the best Pokémon Master in the world, even better than Red himself. He is an adult and is currently surrounded by fans all cheering his name. Gary was there supporting him and making sure he doesn't do something he'll regret. Then the scene changed. Black clouds cover the sun, lightning flash as thunder roared across the sky. And to make things worse, Electric Pokémon came in large numbers and attacked everything until the entire stadium went up in flames.

Before Ash turned into ash, a soft blue glow appears and the flames melted away. A terrified Ash just stood right where he stands and looks at the glow with wonder. After what seemed like an eternity, the glow begins to dim and take shape. The shape it took looks like a crystal dragon to Ash but he had never seen anything like this before.

'It's alright, you were having a nightmare, young Ash,' the crystal dragon spoke. Ash couldn't understand what was going on. But this being a dream is understandable and Ash, now a boy, wasn't sure if he wanted to wake up now.

"What are you? And how do you know my name?" the innocence in his voice echo's across the now vast and empty landscape. The crystal dragon just chuckles before moving to the boy's level.

'Everything would be explained in time, young Ash. Now let me tell you about a great destiny that is yours.' This made Ash excited as many thoughts enter his mind. One of the things he hoped for is to be a great and well-respected Pokémon Master like Red. The crystal dragon sensed this and smiled.

'You would be known as one of the best in many years' time. Don't worry, your dreams would come true and you would be the most respected trainers on the planet. However, this is not enough for when you do complete your dream darkness would come and take everything you hold dear.' Now Ash is getting worried. If this is the price he has to pay to be the best then he doesn't want it.

"Is there any other way for me to make my dream come true? I don't want the darkness to take everything from me." The dragon could tell this boy has a good heart and he knew that this won't change with age, as most do, if the timeline stays the same.

'There is something but this would mean that there is a chance your dream might not come true,' the crystal dragon said with sadness in his voice. Now Ash was more worried than before. What would he do, take the path of certainty and know that it would lead to pain or go for the unknown. His father said to gather as much information as he can before making a decision, though his mother told him to just follow his heart.

"What is it? What would I have to do?" the boy asks while wondering if this is all just in his head. The dragon was about to answer when it tensed. Ash was about to ask it what's wrong but before he could the dragon turns his head towards the boy.

'It seems time has grown too short. It isn't safe here. Go, leave your home and find a place that only you know about. Only then would we continue this talk.' And with that, the crystal dragon begins to glow and Ash closes his eyes.

When he opens them he was back in his room. 'It was just a dream,' he thought and lay back down to fall asleep. However Ash no longer felt safe in the house. Even though he was afraid to be alone before, this feels different; like his heart is saying outside is safer than here and he needs to get out. Without thinking about the lightning, Ash grabs his raincoat, boots, Pokédoll and hat and leaves through the window.

Once outside and on the ground, Ash runs straight into the woods a few yards from the house. He didn't stop running until he reaches an old tree house. Lightning strikes right overhead and Ash screamed and curled into a ball, shaking with his hands on his head. He stayed like that for a few minutes until a voice told him it is safe to move again.

Once inside Ash takes off his rain gear, since his mom doesn't like him wearing wet clothing, and puts them on a hook to dry. He heads towards the back where a small room is. In the small room is a cot with a sleeping bag on top of it. It looks like someone lives here and Ash knew who, him and Gary. This is where they have their campout's when the weather is bad but they never stay here in a thunderstorm.

Clutching his Pokédoll close Ash went to the cot and tried to sleep. The raging storm outside kept him up. Suddenly, a soft blue light enters and moved towards Ash. The light it brings off became so bright the boy had to close his eyes. When he opened them he was in the empty space and the crystal dragon was in front of him.

'It's alright young Ash. You are only asleep,' the dragon told him through what Ash realize now is its thoughts. 'But how can I hear its thoughts?' he wondered.

'It's because I am now connected to your mind. As long as you are asleep, we can talk,' the crystal dragon explains. A thousand thoughts went through Ash's mind but before he could voice them the dragon continues.

'Since our time is short I will get to the point. The darkness that comes after your dreams come true is a darkness that would come no matter what you or anyone would do. This is why I have come to you.' The crystal dragon moves his hand to the left and images started to appear. The images moved so fast Ash didn't really had time to see them but he did catch a few glimpse.

'As you can see, your journey will have its own dangers most trainers, rookie and experience; will never have to face in their lifetime. You are different. Your destiny, that has been decided before you were born, allows you to see things not meant for human eyes. However, I cannot tell what your destiny is. I can tell you that what I am here for will fit in to your destiny quite well.' Ash didn't know what to say. To know you carry a huge responsibility is mind-blowing. He just didn't know if this was really, really, good or really, really, bad.

"If this is going to happen anyway, than why tell me?" the young boy asks while trying to hold back the tears. The dragon sees this and let out a sigh.

'Please do not cry young one. I am telling you this for there might be a way.' Ash dried his tears when he heard that. He didn't need to say anything; his body showed he was listening. The dragon held his head high before continuing.

'There is a way, but you have to promise not to tell anyone about this. If they knew they would probably think you are crazy and that is something I cannot allow.' Being as young as he is, ash didn't understand the danger of the situation but he knew if he wanted answers, you do as you are told, or be stubborn; which ever has the better benefits.

"You have my word. Besides, they will think it's just a dream." The look the dragon gave Ash told him to not take that chance. Ash still didn't understand what the big deal is but he promised and his mother raised him to never break promises unless necessary.

'Very well then, I'll explain. You see, this all happens in the future when you have barely reached your potential, but just a little of it. What I am offering is a change. You must take in training from me in order to unlock this hidden power of yours. But there is a price. Like I have said, if we do this then the future would change and your path will be uncertain. In order to prevent the sudden changes you must catch certain Pokémon at certain times and in certain places or I fear all might as well be lost.'

"But why? Surely the darkness doesn't know about this, do they?" Ash asks a bit confused on this whole thing. The crystal dragon can only shake his head.

'Most of these things will be explained in time; however I can tell you this. The darkness plans to time travel and they seem to have done it before. How it is possible, I do not know. I do know they will know the changes that happen if it's sudden and when they do; our plan will most likely not work. So you see, we must keep this to ourselves and take the path that has been chosen for you until this time has come. Do I make myself clear?'

"Yes sir," young Ash acknowledge before asking a question. "You are a 'sir', right?" The crystal dragon let out a laugh.

'How great it is to be young .Yes I am a 'sir'.' The dragon shakes his head trying to suppress his laugh. 'As for my name, that would be explained in time. Now, have you thought about what you want to do, young Ash?' Ash didn't hesitate on his answer.

"I'll take whatever road I need to protect my mom. She's all I have left," he said the last part more in a whisper. The crystal dragon nodded his head before changing the scene. Now instead of an empty space they, well more Ash, stand in some sort of a room filled with strange flowers.

'Then we shall begin your training. Your first lesson is about Aura.' To make a long story short, the dragon told Ash what Aura is and how he can use it. It took some time but Ash learned the basics before he had to wake up. The dragon told him they will be doing this every night until his Pokémon Journey begins and then it will become scarce. Then he told Ash it was time to wake up.

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When Ash opened his eyes light filled the room he had slept in. He wondered why he was in the tree house but before the memories came back the door to the room flew open. A four year old boy with messy brown hair enters the room and his eyes lock on Ash.

"There you are Ash. Everyone has been looking for you," the boy said while walking up to him. Ash didn't know what to say, the events of the night before were still a bit foggy.

"Hey Ash, where did you get that pretty pink gem in your hand?" At first, Ash was a bit confused but then he looks at his hand and there was a pink gem that was about the size of his hand. He looks at the boy before replying.

"Not sure Gary. Must have picked it up on my way here. You know how I always trip coming down that small hill." Gary didn't say anything but he did grab his friend and pulled him to the door.

"Forget I ask but we have to hurry! Your mother couldn't find you and the rest of town thinks you have been taken away." Now Ash never meant to worry anyone, he just wanted to get to a place that was safe. After stopping Gary from dragging him out of the tree house, Ash grabs his things and put on his rain boots since it's the only shoe he has, then he comes out the door and runs back to town.

"MOM!" he screams once they reach his house. Outside the home were his mother and some people in police uniforms. Delia stopped talking to the police and runs to her son and picks him up. Of course she is upset that he had ran off like that and not tell anyone where he was but he explains to her about his nightmare, leaving out the dragon, and he no longer felt safe in the house anymore so he left.

He learned that there was a break-in and the thieves set the house on fire but the town put the flames out quickly. Still they would have to stay with Gary and his family until the mess has been cleaned-up. When the officers ask Ash where he had been, all he told them was if he tells them than it would no longer be a safe place. For some reason Gary kept quiet about this too.

That night Ash learns that the gem was to help keep his aura under control and he needs to take care of it. And only those he has a bond with can see it. Every night since the crystal dragon taught Ash the ways of aura and some other things. Ash even went to Professor Oak's lab to help take care of Pokémon and to learn more about them. Until the day he starts out on his journey.

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**A/N: Sorry it was cut short. If there are any errors and you know how to fix them please tell me. FYI, I already have a storyline down but writing the first chapter is proving to be difficult. Should Ash catch any pokemon on his first day? What Pokemon, how many and any shinies? And would anyone like to hear the origanal storyline? R&R Please!**


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